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1382 次代码提交

作者 SHA1 备注 提交日期
Minjie Wang ddc2faa547 [Bugfix] Fix gat residual bug (#355)
* fix gat residual bug

* fix the residual addition; output heads; add some shape notations;

* minor

* fix the output head average

* add requests package in requirement
2019-01-12 08:37:01 -05:00
Minjie Wang efae0f97d8 [Model] Improve GAT models (#348)
* two better GAT implementations

* update numbers

* use version switch for spmm

* add missing dropout and output heads
2019-01-11 02:02:06 -05:00
Mufei Li 3a868eb04b [Feature] Max readout and consecutive labeling for networkx (#341)
* Max readout and consecutive labeling

* Delete test_readout.py

* Delete test_basics.py

* Test case and fix

* Recover accidentally removed file

* Fix import order

* Fix test case

* Fix

* Fix

* Fix

* Fix

* Fix

* revert

* Fix

* Fix

* Fix
2019-01-10 12:58:05 -05:00
brett koonce 707334ce85 minor spelling tweaks (#349)
* minor spelling tweaks

* Update CONTRIBUTORS.md
2019-01-10 12:02:31 -05:00
Quan (Andy) Gan e19cd62ecd [Test] Unify tests for different backends (#333)
* test basics

* batched graph & filter, mxnet filter fix

* frame and function; bugfix

* test graph adj and inc matrices

* fixing start = 0 for mxnet

* test index

* inplace update & line graph

* multi send recv

* more tests

* oops

* more tests

* removing old test files; readonly graphs for mxnet still kept

* modifying test scripts

* adding a placeholder for pytorch to reserve directory

* torch 0.4.1 compat fixes

* moving backend out of compute to avoid nose detection

* tests guide

* mx sparse-to-dense/sparse-to-numpy is buggy

* oops

* contribution guide for unit tests

* printing incmat

* printing dlpack

* small push

* typo

* fixing duplicate entries that causes undefined behavior

* move equal comparison to backend
2019-01-05 23:32:33 -05:00
Mufei Li 24bbdb745e [Feature] Reversed Graph and Transform Module (#331)
* reverse a graph

* Reverse a graph

* Fix

* Revert "Fix"

This reverts commit 1728826b4f3a083b76dfc0fdecd2bbf943a971b2.

* Fix

* Fix

* Delete vcs.xml

* Delete Project_Default.xml

* Fix

* Fix

* Fix

* Remove outdated test

* Reorg transform and update reverse (#2)

* Reorg transform and update reverse

* Fix doc and test

* Update test

* Resolve conflict

* CI oriented fix

* Remove outdated import

* Fix import

* Fix import

* define __all__ for wildcard imports

* Fix import

* Address circular imports

* Fix

* Fix test case

* Fix

* Fix

* Remove unused import

* Fix

* Fix

* Fix
2019-01-04 13:51:19 -05:00
Minjie Wang 4bd4d6e348 [Lint] Pylint (#330)
* fix lint for graph_index.py

* pylint for base.py

* pylint for batched_graph.py

* pylint for frame.py; simplify and fix bugs in frame when index is slice type

* pylint for graph.py

* pylint for immutable_graph_index.py

* pylint for init.py

* pylint for rest files in root package

* pylint for _ffi package

* pylint for function package

* pylint for runtime package

* pylint for runtime.ir package

* add pylint to ci

* fix mx tests

* fix lint errors

* fix ci

* fix as requested

* fix lint
2019-01-01 15:15:41 -05:00
Lingfan Yu 2664ed2dff [Bugfix] Fix multiple send recv (#320)
* fix bug: frame append should check itself

* more test case

* fix multi-send-recv bug

* remv msg graph and clean up

* test cases

* more test case

* fix for batchedgraph

* fix bugs: converting from a graph with edges

* fix

* add more operators to utils.Index

* clear frame executor

* change message indicator to a graph level index

* fix test cases

* guard the case that mxnet does not support concat zero shape tensor

* fix bug: avoid convert full slice to numpy

* test multi-send-recv after conversion

* fix as request (partially)

* add dtype, ctx to full_1d

* add slice data to utils.Index

* fix

* more doc string

* fix as requested
2018-12-23 21:35:49 -05:00
Minjie Wang 0d0f44363c [Bugfix] MX utest traversal memory corruption (#312)
* WIP

* temp fix mx traversal memory crash bug
2018-12-16 21:07:59 -08:00
Minjie Wang f35ac5443e [Graph][Model] Cache adj & inc; MX GCN (#307)
* add cache to adj and incmat

* Fix bug in cached adj/inc

* mx gcn spmv runnable; acc debugging...

* fix bug in mx gcn that loss is not correctly calculated

* fix mx utest

* fix as requested

* use raw parameter tensors rather than dense layer

* fix dropout

* Add numbers in readme
2018-12-16 22:51:01 -05:00
Haibin Lin e2926544b6 [Graph] Better string repr (#311) 2018-12-16 12:23:49 -05:00
Haibin Lin 30107407fd add prefetcher for neighbor sampler (#298) 2018-12-15 19:14:17 -08:00
Lingfan Yu 0cbe521b99 [Doc] Fix document building for multiple tensor backends (#301)
* remove loading backend in sse

* build mxnet in a second run

* a third run to fix everything

* fix docstring in sampler

* fix docstring in transformer

* README for doc build

* some reordering and printing

* use filename_pattern instead of ignore_pattern to reduce warning at the cost of redundant work...

* add env var to use mxnet in Jenkinsfile

* remove step 3, it's already fixed by previous commit
2018-12-12 11:07:46 -05:00
Minjie Wang af23c45726 [Release] update version (#297)
* update version; add news.md; modify contributing.md

* change urls to dmlc
2018-12-11 15:40:51 -05:00
Da Zheng 18ed7868fe [Doc] update neighbor sampler doc. (#287) 2018-12-11 12:48:22 -05:00
Minjie Wang 597ac7f8b5 [Release] v0.1.3 (#288)
* 0.1.2 release

* oops

* more fixes on windows

* [Bugfix] fix download dir (#275)

* fix download dir

* add doc for the env var

* windows 7 -> 10

* doc update

* [Bugfix] Fix conversion from networkx (#286)

* fix from_nx when no edge id available

* add test cases

* more detailed tests

* more comments

* [Bugfix] Switch to sparse_coo_matrix for torch 1.0+ (#282)

* switch to sparse_coo_matrix for torch 1.0+

* fix bug when the version is 0.4.1.post2

* change to distutils
2018-12-11 01:30:47 -05:00
Gan Quan 37feb479fd [Release] 0.1.2 updates (#276)
* 0.1.2 release

* oops

* more fixes on windows

* [Bugfix] fix download dir (#275)

* fix download dir

* add doc for the env var
2018-12-07 01:54:13 -05:00
Da Zheng c0d1f8e43b small fixes in the immutable graph index. (#271)
* small fix in immutable graph index.

* minor fix.
2018-12-06 19:01:14 -08:00
Sheng Zha f720ce13e1 [Build] support universal wheel on linux (#272) 2018-12-06 18:06:58 -05:00
Da Zheng 1bbc885b40 move batcher to examples. (#269)
* move pytorch code to examples.

* fix.

* fix tutorial
2018-12-06 06:45:27 -08:00
Da Zheng 7aa494b3bc [Bugfix][Doc] explain the batch dimension in the doc and many fix (#266)
* add more unit tests for mxnet.

* fix.

* explain the batch dimension.

* update doc.

* disable unit tests on DFS.

* fix graph traversal.
2018-12-06 00:48:57 -05:00
Minjie Wang 612a7fb996 [Release] setup version (#264) 2018-12-05 19:33:06 -05:00
Minjie Wang c620bfc2b7 [Doc] faq & env (#263)
* faq & env

* add update version script; 0.0.1 -> 0.1.0
2018-12-05 19:18:33 -05:00
Da Zheng 063ed69cdf [BUGFIX] fix a bug in creating immutable graph index. (#251)
* fix a bug in creating immutable graph index.

* fix for new changes in the backend API.

* fix for creating immutable graph index from coo matrix.

* retrigger
2018-12-05 17:51:50 -05:00
Minjie Wang 2194b7dfa6 [Bugfix] edge order is not preserved when converting from edge list (#262) 2018-12-05 17:41:26 -05:00
Lingfan Yu a1d50f0f53 [Refactor] Rename before release (#261)
* include/dgl/runtime

* include

* src/runtime

* src/graph

* src/scheduler

* src

* clean up CMakeLists

* further clean up in cmake

* install commands

* python/dgl/_ffi/_cython

* python/dgl/_ffi/_ctypes

* python/dgl/_ffi

* python/dgl

* some fix

* copy right
2018-12-05 16:45:36 -05:00
VoVAllen cd907cddfa [Tutorial] Add sse tutorial & MXNet Tutorial CI (#252)
* add sse tutorial

* add mxnet tutorial ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* Fix ci

* Fix ci

* Fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* Fix CI

Fix CI image

* permission fix

* fix a bug in the code.

* small fix

* fix doc

* fix ci

* shorten the iters

* fix

* remove extra file

* add load_backend api to dynamically switch to another backend

* try fix

* fix tutorial

* fix tutorial

* fix bug in tutorial
2018-12-05 16:21:44 -05:00
Da Zheng 899d125bb1 Add tests for MXNet and throw NotImplementedError if not implemented (#258)
* add more unit tests for mxnet.

* fix.
2018-12-05 10:41:33 -08:00
Da Zheng 7c7cc7e0c2 [sampler] Adjust the sampler API for the future extension. (#243)
* return seed ids.

* fix tests.

* implement.
2018-12-05 10:05:10 -08:00
Lingfan Yu 378c264561 [Model] Fix GCN Normalization (#249)
* WIP

* lr -> 0.01

* new cora dataset

* normalization code

* minor format change

* normalization factor for deg bucket
2018-12-05 12:32:10 -05:00
Minjie Wang 21255b6528 [Bugfix] tolist and dependencies in dgl.data (#239)
* change Index.tolist -> Index.tonumpy; fix bug in traversal; remove dependencies in data

* fix import

* fix __all__ and some docstring
2018-12-05 12:20:59 -05:00
Minjie Wang eafcb7e7f5 [Bugfix][MXNet] Fix edge order and builtin max bug in mx (#247)
* Fix edge order and builtin max bug in mx

* fix as requested
2018-12-05 01:32:54 -08:00
Lingfan Yu 274e1082f5 [Doc] API doc string for many components (#245)
* builtin function docstring

* init docstring

* view docstring

* add init to index and fix

* node /edge feature

* Example -> Examples

* fix func hyperlink

* traversal

* fix

* from/to_networkx docstring

* minor

* fix duplicate label

* comment about tensor framework

* from scipy sparse matrix

* fix format errors
2018-12-04 17:52:00 -05:00
Mufei Li 7cca500787 [Doc] Computing with DGLGraph (#212)
* Docs for graph computing

* Docs for graph computing

* Fix

* WIP

* update the docstring
2018-12-04 16:51:46 -05:00
Da Zheng c99f423718 [Sampler] extend sampler (#238) 2018-12-04 16:46:26 -05:00
Lingfan Yu 455ea48570 [Bugfix] Conversion between networkx and DGLGraph (#244)
* copy feature to networkx

* fix to_network for multi-graph

* test case for nx conversion

* iterate over Index returns plain int instead of numpy.int64

* fix from_network multi-edge bug
2018-12-04 16:19:11 -05:00
Da Zheng a5a35d1f7a [Sampler] improve random shuffle performance in sampler (#228)
* fix.

* make it generic.

* add the API.

* fix.

* remove mxnet.
2018-12-04 09:24:32 -08:00
Da Zheng dafe46710b [Bug][MXNet] fix an API in immutable graph index. (#233) 2018-12-04 00:37:18 -05:00
HQ b1e8d95e99 [Doc] LGNN tutorial (#210)
* tutorial notebook added

* lg tutorial cleaned up

* dataset scaffold

* move dataloader to data

* fix model

* remove todo

* utils seperated

* [model]line graph new implementation + tutorial + binary sub graph dataset

* [tutorial] line graph sphinx scaffold

* [tutorial] lgnn tutorial improved

* [tutorial] remove notebook

* [tutorial] fix lg and gcn links

* [tutorial] fix random seed

* [tutorial]fix

* WIP

* code refactor done

* new mini dataset; remove utils code

* fix

* word fix

* fix link

* minor fix

* minor fix

* minor fix
2018-12-03 17:59:50 -05:00
Da Zheng 2c170a8c17 [Graph][Bugfix] Fix the API of map_to_subgraph_nid (#226)
* correct vid mapping API.

* fix sse.
2018-12-03 17:16:35 -05:00
Lingfan Yu b0c76d48be [Bug] fix __slots__ in view.py (#230) 2018-12-03 13:28:22 -05:00
Lingfan Yu 52ed09a392 [Bug] Fix inplace update (#221)
* inplace write row op and executor

* update scheduler and graph to use inplace write

* fix

* fix bug

* test case for inplace

* fix bugs for inplace apply node/edge

* fix comments

* th.allclose -> U.allclose
2018-12-02 19:14:39 -05:00
Gan Quan 5680f8dc13 [DOC] Documentation strings for graph mutation, queries, and subgraphing (#207)
* docstrings for graph mutation & queries

* [Doc] contrib.sampler. (#200)

* subgraph docs

* updates
2018-12-02 14:41:25 -05:00
Minjie Wang 57daf9c9a6 [Graph] small fix on the all index (#219) 2018-12-02 13:39:04 -05:00
Da Zheng 57b07fce92 [Model] Accelerate SSE (#172)
* lazy eval edge ids.

* parallelize node id lookup.

* fix a bug.

* use mxnet for index.

* use update_all in the subgraph training.

* sample neighbors.

* Revert "parallelize node id lookup."

This reverts commit e661f69bb06cb5a7c246f0e106f245e27800e220.

* update README.

* cache subgraphs.

* support all degrees.

* cache adj in CPU.

* fix a bug in sse.

* print.

* raise error on mutable graphs.

* measure train time per epoch.

* fix a bug in graph_index.

* remove readonly in DGLSubGraph.

* cache subgraph properly.

* accelerate getting adjacency.

* split infer.

* lazy eval edges.

* specify inference mode.

* update for new sampler.

* use new mxnet sampling api.

* fix indent.

* remove profiling code.

* remove mxnet from sampler.

* return a lambda function for graph edges.

* add docs for immutable subgraph.

* Revert "return a lambda function for graph edges."

This reverts commit 0de5d7f100e230c518a3fb8976a6227f474d09ee.

* get parent_eid.
2018-12-02 12:43:25 -05:00
Haibin Lin 5278220f85 update s3 links (#215) 2018-12-02 20:48:29 +08:00
Lingfan Yu 53ea03ad82 [Doc] Fix doc bug and warning (#213)
* fix dgmg tutorial indentation

* bug in incidence_matrix docstring

* remove print
2018-12-01 18:58:56 -05:00
Lingfan Yu 0f121eeb76 [Doc] RGCN tutorial (#206)
* rgcn tutorial

* data processing for rgcn

* many fix

* requirements for rgcn tutorial

* fix comments

* description of rgcn dataset

* author

* bug fix

* move all dataset to s3
2018-12-01 14:58:13 -05:00
Haibin Lin cccc2339c1 [Dataset] update s3 links (#209) 2018-12-01 14:45:30 -05:00
VoVAllen 91141a9826 [Dataset] Move file from dropbox to s3 (and fix ci fail due to sst dataset) (#205)
* move file from dropbox to s3

* fix ci and move sst to s3

* remove blank line
2018-11-30 19:44:55 -05:00